SAGE Genie

SAGE Genie

The SAGE Genie website provides highly intuitive,
visual displays of human and mouse gene
expression, based on a unique analytical process (Boon et al.)
that reliably matches SAGE tags, 10 or 17 nucleotides in length,
to known genes. Recently, with the construction and incorporation of a reference
database of SNP-associated alternative tags into SAGE Genie (Silva et al.),
the interpretation of tag to human gene mapping has been enhanced.

The SAGE Anatomic Viewer
visually displays the relative expression of a given gene in normal and malignant
tissues of the human body. In addition, there is access to:

The Digital Northern, which shows the relative
expression of the gene in each library.

The Ludwig Transcript (LT) Viewer,
which visually represents a particular transcript with up to four possible
virtual SAGE tag locations (starting from the 3' end) and locations of internally primed
or alternatively polyadenylated transcripts.

The mSAGE Expression Matrix
visually displays the relative expression of a given gene
through stages of mouse development. In addition, there is access to:

The Digital Northern, which shows the relative
expression of the gene in each library.

The Ludwig Transcript (LT) Viewer,
which visually represents a particular transcript with up to four possible
virtual SAGE tag locations (starting from the 3' end) and locations of
internally primed or alternatively polyadenylated transcripts.

The mSAGE Absolute Level Lister lists all mouse SAGE libraries,
organized by either tissue (normal or malignant) or developmental stage, and links to the distribution of
transcript expression levels in any given library.

The majority of human libraries are short whereas the majority of
mouse libraries are "long".

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Several mouse developmental libraries are prepared by the SAGELite method.
SAGELite is an extension of the long Sage protocol that includes a PCR-based amplification
stage to allow the use of 10ng to 100ng of total RNA to produce a Sage library. However, it
has been observed that a significant bias
incurred by this amplification process.

SAGE Genie Collaborators

SAGE Genie was produced as part of the NCI CGAP SAGE project with
collaborators from
Johns Hopkins University, the Ludwig Institute for Cancer Research, Sao Paulo Branch,
the University of Texas MD Anderson Cancer Center, and the Genome Sciences Center of the BCCRC.